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Although you might have found a solution to this issue long ago, just wanted to leave my answer here for the benefit of others. I had lot of surface matching/intersection problems as well to the extent I may have to redraw a multi-story building. The surface matching tools through SketchUp always caused several errors. The workaround was to use the OpenStudio Measure "SurfaceMatching" through "Apply Measures Now" in OpenStudio interface to your model. This solved almost all the surface matching errors. Please note that this should be applied to the model without doing any surface matching/intersections through Sketchup/OpenStudio Plugin.